# BioPerl module for TribeMCL
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon <shawnh@fugu-sg.org>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::TribeMCL
=head1 SYNOPSIS
use Bio::Tools::Run::TribeMCL;
use Bio::SearchIO;
# 3 methods to input the blast results
# straight forward raw blast output (NCBI or WU-BLAST)
my @params = ('inputtype'=>'blastfile');
# OR
# markov program format
# protein_id1 protein_id2 evalue_magnitude evalue_factor
# for example:
# proteins ENSP00000257547 and ENSP00000261659
# with a blast score evalue of 1e-50
# and proteins O42187 and ENSP00000257547
# with a blast score evalue of 1e-119
# entry would be
my @array = [[qw(ENSP00000257547 ENSP00000261659 1 50)],
[qw(O42187 ENSP00000257547 1 119)]];
my @params = ('pairs'=>\@array,I=>'2.0');
# OR
# pass in a searchio object
# slowest of the 3 methods as it does more rigourous parsing
# than required for us here
my $sio = Bio::SearchIO->new(-format=>'blast',
-file=>'blast.out');
my @params=('inputtype'=>'searchio',I=>'2.0');
# you can specify the path to the executable manually in the following way
my @params=('inputtype'=>'blastfile',I=>'2.0',
'mcl'=>'/home/shawn/software/mcl-02-150/src/shmcl/mcl',
'matrix'=>'/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# OR
$fact->matrix_executable('/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
$fact->mcl_executable('/home/shawn/software/mcl-02-150/src/shmcl/mcl');
# to run
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# Run the program
# returns an array reference to clusters where members are the ids
# for example :2 clusters with 3 members per cluster:
# $fam = [ [mem1 mem2 mem3],[mem1 mem2 mem3]]
# pass in either the blastfile path/searchio obj/the array ref to scores
my $fam = $fact->run($sio);
# print out your clusters
for (my $i = 0; $i <scalar(@{$fam}); $i++){
print "Cluster $i \t ".scalar(@{$fam->[$i]})." members\n";
foreach my $member (@{$fam->[$i]}){
print "\t$member\n";
}
}
=head1 DESCRIPTION
TribeMCL is a method for clustering proteins into related groups,
which are termed 'protein families'. This clustering is achieved by
analysing similarity patterns between proteins in a given dataset, and
using these patterns to assign proteins into related groups. In many
cases, proteins in the same protein family will have similar
functional properties.
TribeMCL uses a novel clustering method (Markov Clustering or MCL)
which solves problems which normally hinder protein sequence
clustering.
Reference:
Enright A.J., Van Dongen S., Ouzounis C.A; Nucleic Acids
Res. 30(7):1575-1584 (2002)
You will need tribe-matrix (the program used to generate the matrix
for input into mcl) and mcl (the clustering software) available at:
http://www.ebi.ac.uk/research/cgg/tribe/ or
http://micans.org/mcl/.
Future Work in this module: Port the tribe-matrix program into perl so
that we can enable have a SearchIO kinda module for reading and
writing mcl data format
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
# Let the code begin...
package Bio::Tools::Run::TribeMCL;
use vars qw($AUTOLOAD @ISA $PROGRAMDIR
@TRIBEMCL_PARAMS @MATRIXPROGRAM_PARAMS @MCLPROGRAM_PARAMS
@OTHER_SWITCHES %OK_FIELD
$MATRIXPROGRAM_NAME $MCLPROGRAM_NAME
$MCLPROGRAM $MATRIXPROGRAM
);
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Cluster::SequenceFamily;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Run::WrapperBase;
use Bio::Annotation::DBLink;
use Bio::Seq;
use Bio::Species;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
# You will need to enable mcl and tribe-matrix to use this wrapper. This
# can be done in (at least) two ways:
#
# 1. define an environmental variable TRIBEDIR
# export TRIBEDIR =/usr/local/share/mclbin/
# where the tribe-matrix and mcl programs are located.
#you probably need to copy them individually to the same directory
#if the installation puts them in different directories. or simply put them in
#your standard /usr/local/bin
#
# 2. include a definition of an environmental variable TRIBEDIR in
# every script that will use TRIBEMCL.pm
# $ENV{TRIBEDIR} = '/usr/local/share/mclbin/;
#
#3. Manually set the path to the executabes in your code:
#
#my @params=('inputtype'=>'blastfile',I=>'2.0','
# mcl'=>'/home/shawn/software/mcl-02-150/src/shmcl/mcl','
# matrix'=>'/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
#my $fact = Bio::Tools::Run::TribeMCL->new(@params);
#or
#$fact->matrix_executable('/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
#$fact->mcl_executable('/home/shawn/software/mcl-02-150/src/shmcl/mcl');
BEGIN {
$MATRIXPROGRAM_NAME = 'tribe-matrix';
$MCLPROGRAM_NAME = 'mcl';
if (defined $ENV{TRIBEDIR}) {
$PROGRAMDIR = $ENV{TRIBEDIR} || '';
$MCLPROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,$MCLPROGRAM_NAME.($^O =~ /mswin/i ?'.exe':''));
$MATRIXPROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,$MATRIXPROGRAM_NAME.($^O =~ /mswin/i ?'.exe':''));
}
@TRIBEMCL_PARAMS = qw(inputtype hsp hit scorefile blastfile description_file searchio pairs mcl matrix weight description family_tag use_db);
@MATRIXPROGRAM_PARAMS = qw(ind out chunk);
@MCLPROGRAM_PARAMS = qw(I t P R pct o);
@OTHER_SWITCHES = qw(verbose quiet);
# Authorize attribute fields
foreach my $attr (@TRIBEMCL_PARAMS, @MATRIXPROGRAM_PARAMS,
@MCLPROGRAM_PARAMS, @OTHER_SWITCHES) {
$OK_FIELD{$attr}++;
}
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/MCL/i) {
$self->mcl_executable($value);
next;
}
if ($attr =~ /MATRIX/i){
$self->matrix_executable($value);
next;
}
$self->$attr($value);
}
defined($self->weight) || $self->weight(200);
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 mcl_executable
Title : mcl_executable
Usage : $self->mcl_executable()
Function: get set for path to mcl executable
Returns : String or undef if not installed
Args : [optional] string of path to executable
[optional] boolean to warn on missing executable status
=cut
sub mcl_executable{
my ($self,$exe,$warn) = @_;
if( defined $exe ) {
$self->{'_mcl_exe'} = $exe;
}
unless( defined $self->{'_mcl_exe'} ) {
# this would be the name set in the BEGIN block
if( $MCLPROGRAM && -e $MCLPROGRAM && -x $MCLPROGRAM ) {
$self->{'_mcl_exe'} = $MCLPROGRAM;
} else {
my $exe;
if( ( $exe = $self->io->exists_exe($MCLPROGRAM_NAME) ) &&
-x $exe ) {
$self->{'_mcl_exe'} = $exe;
} else {
$self->warn("Cannot find executable for $MCLPROGRAM_NAME") if $warn;
$self->{'_mcl_exe'} = undef;
}
}
}
$self->{'_mcl_exe'};
}
=head2 matrix_executable
Title : matrix_executable
Usage : $self->matrix_executable()
Function: get set for path to tribe-matrix executable
Returns : String or undef if not installed
Args : [optional] string of path to executable
[optional] boolean to warn on missing executable status
=cut
sub matrix_executable{
my ($self,$exe,$warn) = @_;
if( defined $exe ) {
$self->{'_matrix_exe'} = $exe;
}
unless( defined $self->{'_matrix_exe'} ) {
# this would be the name set in the BEGIN block
if( $MATRIXPROGRAM && -e $MATRIXPROGRAM && -x $MATRIXPROGRAM ) {
$self->{'_matrix_exe'} = $MATRIXPROGRAM;
} else {
my $exe;
if( ( $exe = $self->io->exists_exe($MATRIXPROGRAM_NAME) ) &&
-x $exe ) {
$self->{'_matrix_exe'} = $exe;
} else {
$self->warn("Cannot find executable for $MATRIXPROGRAM_NAME")
if $warn;
$self->{'_matrix_exe'} = undef;
}
}
}
$self->{'_matrix_exe'};
}
=head2 run
Title : run
Usage : $self->run()
Function: runs the clustering
Returns : Array Ref of clustered Ids
Args :
=cut
sub run {
my ($self,$input) = @_;
if($self->description_file){
$self->_setup_description($self->description_file);
}
my $file = $self->_setup_input($input);
defined($file) || $self->throw("Error setting up input ");
#run tribe-matrix to generate matrix for mcl
my ($index_file, $mcl_infile) = $self->_run_matrix($file);
$self->throw("tribe-matrix not run properly as index file is missing")
unless (-e $index_file);
$self->throw("tribe-matrix not run properly as matrix file is missing")
unless (-e $mcl_infile);
#run mcl
my $clusters = $self->_run_mcl($index_file,$mcl_infile);
my $families;
if($self->description){
my %consensus = $self->_consensifier($clusters);
$families = $self->_generate_families($clusters,\%consensus);
}
else {
$families = $self->_generate_families($clusters);
}
return @{$families};
}
sub _generate_families {
my ($self,$clusters,$consensus) = @_;
my $family_tag = $self->family_tag || "TribeFamily";
my @fam;
if($consensus){
my %description = %{$self->description};
my %consensus = %{$consensus};
for(my $i = 0; $i < scalar(@{$clusters}); $i++){
my @mem;
foreach my $member (@{$clusters->[$i]}){
my $mem = Bio::Seq->new(-id=>$member,
-alphabet=>"protein",
-desc=>$description{$member}->[1]);
my $annot = Bio::Annotation::DBLink->new(-database=>$description{$member}->[0],
-primary_id=>$member);
$mem->annotation->add_Annotation('dblink',$annot);
#store species information
my $taxon_str = $description{$member}->[2];
#parse taxon info into hash
my %taxon;
$taxon_str=~s/=;/=undef;/g if $taxon_str;
%taxon = map{split '=',$_}split';',$taxon_str if $taxon_str;
my $name = $taxon{'taxon_common_name'};
my @classification = $taxon{'taxon_classification'} ? split(':',$taxon{'taxon_classification'}) : ();
my $tax_id = $taxon{'taxon_id'};
my $sub_species = $taxon{'taxon_sub_species'};
my $species = Bio::Species->new();
$species->common_name($name) if $name; #*** should this actually be scientific_name() ?
$species->sub_species($sub_species) if $sub_species;
$species->ncbi_taxid($tax_id) if $tax_id;
$species->classification(@classification) if @classification;
$mem->species($species);
push @mem, $mem;
}
my $id = $family_tag."_".$i;
my $fam = Bio::Cluster::SequenceFamily->new(-family_id=>$id,
-description=>$consensus{$i}{desc},
-annotation_score=>$consensus{$i}{conf},
-members=>\@mem);
push @fam, $fam;
}
return \@fam;
}
else {
for(my $i = 0; $i < scalar(@{$clusters}); $i++){
my @mem;
foreach my $member (@{$clusters->[$i]}){
my $mem = Bio::Seq->new(-id=>$member,
-alphabet=>"protein");
push @mem, $mem;
}
my $id = $family_tag."_".$i;
my $fam = Bio::Cluster::SequenceFamily->new(-family_id=>$id,
-members=>\@mem);
push @fam, $fam;
}
return \@fam;
}
}
sub _consensifier {
my ($self,$clusters) = @_;
eval {
require "Algorithm/Diff.pm";
};
if($@){
$self->warn("Algorith::Diff is needed to run TribeMCL");
return undef;
}
my %description = %{$self->description};
my %consensus;
my $best_annotation;
my %use_db;
if($self->use_db){
foreach my $key(split(',',$self->use_db)){
$use_db{$key}++;
}
}
CLUSTER:
for(my $i = 0; $i < scalar(@{$clusters}); $i++){
my @desc;
my @orig_desc;
my $total_members = scalar(@{$clusters->[$i]});
foreach my $member(@{$clusters->[$i]}){
#if specify which dbs to use for consensifying
if($self->use_db){
if($use_db{$description{$member}->[0]}){
push @desc, $description{$member}->[1] if $description{$member}->[1];
push @orig_desc, $description{$member}->[1] if $description{$member}->[1];
}
}
else {
push @desc, $description{$member}->[1] if $description{$member}->[1];
push @orig_desc, $description{$member}->[1] if $description{$member}->[1];
}
}
if($#desc < 0){ #truly unknown
$consensus{$i}{desc} = "UNKNOWN";
$consensus{$i}{conf} = 0;
next CLUSTER;
}
if($#desc == 0){#only a single description
$consensus{$i}{desc} = grep(/S+/,@desc);
$consensus{$i}{desc} = $consensus{$i}{desc} || "UNKNOWN";
if ($consensus{$i}{desc} eq "UNKNOWN") {
$consensus{$i}{conf} = 0;
} else {
$consensus{$i}{conf} = 100 * int(1/$total_members);
}
next CLUSTER;
}
#all the same desc
my %desc = ();
foreach my $desc (@desc) { $desc{$desc}++; }
if ( (keys %desc) == 1 ) {
my ($best_annotation,) = keys %desc;
my $n = grep($_ eq $best_annotation, @desc);
my $perc= int( 100*($n/$total_members) );
$consensus{$i}{desc} = $best_annotation;
$consensus{$i}{conf} = $perc;
next CLUSTER;
}
my %lcshash = ();
my %lcnext = ();
while (@desc) {
# do an all-against-all LCS (longest commong substring) of the
# descriptions of all members; take the resulting strings, and
# again do an all-against-all LCS on them, until we have nothing
# left. The LCS's found along the way are in lcshash.
#
# Incidentally, longest common substring is a misnomer, since it
# is not guaranteed to occur in either of the original strings. It
# is more like the common parts of a Unix diff ...
for (my $i=0;$i<@desc;$i++) {
for (my $j=$i+1;$j<@desc;$j++){
my @list1=split(" ",$desc[$i]);
my @list2=split(" ",$desc[$j]);
my @lcs=Algorithm::Diff::LCS(\@list1,\@list2);
my $lcs=join(" ",@lcs);
$lcshash{$lcs}=1;
$lcnext{$lcs}=1;
}
}
@desc=keys(%lcnext);
undef %lcnext;
}
my ($best_score, $best_perc)=(0, 0);
my @all_cands=sort {length($b) <=>length($a)} keys %lcshash ;
foreach my $candidate_consensus (@all_cands) {
my @temp=split(" ",$candidate_consensus);
my $length=@temp; # num of words in annotation
# see how many members of cluster contain this LCS:
my ($lcs_count)=0;
foreach my $orig_desc (@orig_desc) {
my @list1=split(" ",$candidate_consensus);
my @list2=split(" ",$orig_desc);
my @lcs=Algorithm::Diff::LCS(\@list1,\@list2);
my $lcs=join(" ",@lcs);
if ($lcs eq $candidate_consensus ||
index($orig_desc,$candidate_consensus) != -1 # addition;
# many good (single word) annotations fall out otherwise
) {
$lcs_count++;
# Following is occurs frequently, as LCS is _not_ the longest
# common substring ... so we can't use the shortcut either
# if ( index($orig_desc,$candidate_consensus) == -1 ) {
# warn "lcs:'$lcs' eq cons:'$candidate_consensus' and
# orig:'$orig_desc', but index == -1\n"
# }
}
}
my $perc_with_desc=(($lcs_count/$total_members))*100;
my $perc=($lcs_count/$total_members)*100;
my $score=$perc + ($length*14); # take length into account as well
$score = 0 if $length==0;
if (($perc_with_desc >= 40) && ($length >= 1)) {
if ($score > $best_score) {
$best_score=$score;
$best_perc=$perc;
$best_annotation=$candidate_consensus;
}
}
}
if ($best_perc==0 || $best_perc >= 100 ) {
$best_perc='NA';
}
if ($best_annotation eq '') {
$best_annotation = 'AMBIGUOUS';
}
$consensus{$i}{desc} = $best_annotation;
$consensus{$i}{conf} = $best_perc;
}
return %consensus;
}
sub _setup_description {
my ($self,$file) = @_;
my $goners='().-';
my $spaces= ' ' x length($goners);
my $filter = "tr '$goners' '$spaces' < $file";
open (FILE,"$filter | ") || die "$filter: $!";
my %description;
while(<FILE>){
chomp;
my ($db,$acc,$description,$taxon_str) = split("\t",$_);
$description || $self->throw("Wrongly formated description file");
$description = $self->_apply_edits($description);
if($description{$acc}){
$self->warn("Duplicated entry $acc in description file, overwriting..");
}
$description{$acc} = [$db,$description,$taxon_str];
}
$self->description(\%description);
}
sub as_words {
#add ^ and $ to regexp
my (@words);
my @newwords=();
foreach my $word (@words) { push @newwords, "^$word\$" };
}
sub _apply_edits {
my ($self,$desc) = @_;
my @deletes = ( 'FOR\$', 'SIMILAR TO\$', 'SIMILAR TO PROTEIN\$',
'RIKEN.*FULL.*LENGTH.*ENRICHED.*LIBRARY',
'\w*\d{4,}','HYPOTHETICAL PROTEIN'
);
my @newwords = &as_words(qw(NOVEL PUTATIVE PREDICTED
UNNAMED UNNMAED ORF CLONE MRNA
CDNA EST RIKEN FIS KIAA\d+ \S+RIK IMAGE HSPC\d+
FOR HYPOTETICAL HYPOTHETICAL));
push @deletes, @newwords;
foreach my $re ( @deletes ) { $desc=~s/$re//g; }
#Apply some fixes to the annotation:
$desc=~s/EC (\d+) (\d+) (\d+) (\d+)/EC $1.$2.$3.$4/;
$desc=~s/EC (\d+) (\d+) (\d+)/EC $1.$2.$3.-/;
$desc=~s/EC (\d+) (\d+)/EC $1\.$2.-.-/;
$desc=~s/(\d+) (\d+) KDA/$1.$2 KDA/;
return $desc;
}
=head2 _run_mcl
Title : _run_mcl
Usage : $self->_run_mcl()
Function: internal function for running the mcl program
Returns : Array Ref of clustered Ids
Args : Index_file name, matrix input file name
=cut
sub _run_mcl {
my ($self,$ind_file,$infile) = @_;
my $exe = $self->mcl_executable || $self->throw("mcl not found.");
my $cmd = $exe . " $infile";
unless (defined $self->o) {
my ($fh,$o) = $self->io->tempfile(-dir=>$self->tempdir);
$self->o($o);
# file handle not use later so deleted
close($fh);
undef $fh;
}
unless (defined $self->I) {
$self->I(3.0);
}
foreach my $param (@MCLPROGRAM_PARAMS) {
if (defined $self->$param) {
$cmd .= " -$param ".$self->$param;
}
}
if($self->quiet ||
($self->verbose < 0)){
$cmd .= " -V all";
if( $^O !~ /Mac/ && $^O !~ /Win/ ) {
$cmd .= ' 2> /dev/null';
}
}
my $status = system($cmd);
$self->throw( "mcl call ($cmd) crashed: $? \n") unless $status==0;
my $families = $self->_parse_mcl($ind_file,$self->o);
return $families;
}
=head2 _run_matrix
Title : _run_matrix
Usage : $self->_run_matrix()
Function: internal function for running the tribe-matrix program
Returns : index filepath and matrix file path
Args : filepath of parsed ids and scores
=cut
sub _run_matrix {
my ($self,$parse_file) = @_;
my $exe = $self->matrix_executable || $self->throw("tribe-matrix not found.");
my $cmd = $exe . " $parse_file";
unless (defined $self->ind) {
my ($fh,$indexfile) = $self->io->tempfile(-dir=>$self->tempdir);
$self->ind($indexfile);
# file handle not use later so deleted
close($fh);
undef $fh;
}
unless (defined $self->out) {
my ($fh,$matrixfile) = $self->io->tempfile(-dir=>$self->tempdir);
$self->out($matrixfile);
# file handle not use later so deleted
close($fh);
undef $fh;
}
foreach my $param (@MATRIXPROGRAM_PARAMS) {
if (defined $self->$param) {
$cmd .= " -$param ".$self->$param;
}
}
$cmd .= " > /dev/null";
my $status = system($cmd);
$self->throw( "tribe-matrix call ($cmd) crashed: $? \n") unless $status==0;
return ($self->ind,$self->out);
}
=head2 _setup_input
Title : _setup_input
Usage : $self->_setup_input()
Function: internal function for running setting up the inputs
needed for running mcl
Returns : filepath of parsed ids and scores
Args :
=cut
sub _setup_input {
my ($self,$input) = @_;
my ($type,$rc);
my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir);
$type = $self->inputtype();
if($type=~/scorefile/i){
-e $self->scorefile ||
$self->throw("Scorefile doesn't seem to exist or accessible");
return $self->scorefile;
}
if($type =~/blastfile/i){
$self->blastfile($input);
$rc = $self->_parse_blastfile($self->blastfile,$tfh);
}
elsif($type=~/searchio/i){
$self->searchio($input);
$rc = $self->_get_from_searchio($self->searchio,$tfh);
}
elsif($type=~/pairs/i) {
$self->pairs($input);
for my $line (@{ $self->pairs }){
print $tfh join("\t",@{$line}), "\n";
$rc++;
}
}
elsif($type =~/hsp/i) {
$self->hsp($input);
$rc = $self->_get_from_hsp($self->hsp,$tfh);
}
elsif($type=~/hit/i){
$self->hit($input);
$rc = $self->_get_from_hit($self->hit,$tfh);
}
else {
$self->throw("Must set inputtype to either blastfile,searchio or ".
"paris using \$fact->blastfile |\$fact->searchio| \$fact->pairs");
}
unless ( $rc ) {
$self->throw("Need inputs for running tribe mcl, nothing provided");
}
close($tfh);
$tfh= undef;
return $outfile;
}
=head2 _get_from_hsp
Title : _get_from_hsp
Usage : $self->_get_from_hsp()
Function: internal function for getting blast scores from hsp
Returns : array ref to ids and score [protein1 protein2 magnitude factor]
Args : L<Bio::Search::HSP::GenericHSP>
=cut
sub _get_from_hsp {
my ($self,$hsp,$tfh) = @_;
my @array;
my $count;
foreach my $pair (@{$hsp}){
my $sig = $pair->score;
$sig =~ s/^e-/1e-/g;
my $expect=sprintf("%e",$sig);
if ($expect==0){
my $wt = $self->weight;
$expect=sprintf("%e","1e-$wt");
}
my $first=(split("e-",$expect))[0];
my $second=(split("e-",$expect))[1];
print $tfh join("\t", $pair->feature1->seq_id,
$pair->feature2->seq_id,int($first),
int($second) ), "\n";
$count++;
}
return $count;
}
sub _get_from_hit {
my ($self,$hit,$tfh) = @_;
my $count;
foreach my $pair(@{$hit}){
my $sig = $pair->raw_score;
$sig =~s/^e-/1e-/g;
my $expect = sprintf("%e",$sig);
if ($expect==0){
my $wt = $self->weight;
$expect=sprintf("%e","1e-$wt");
}
my $first=(split("e-",$expect))[0];
my $second=(split("e-",$expect))[1];
print $tfh join("\t",$pair->name,$pair->description,int($first),int($second)),"\n";
$count++;
}
return $count;
}
=head2 _get_from_searchio
Title : _get_from_searchio
Usage : $self->_get_from_searchio()
Function: internal function for parsing blast scores from searchio object
Returns : array ref to ids and score [protein1 protein2 magnitude factor]
Args : L<Bio::Tools::SearchIO>
=cut
sub _get_from_searchio {
my ($self,$sio,$tfh) = @_;
my @array;
my $count;
while( my $result = $sio->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
my $sig = $hsp->evalue;
$sig =~ s/^e-/1e-/g;
my $expect=sprintf("%e",$sig);
if ($expect==0){
my $wt = $self->weight;
$expect=sprintf("%e","1e-$wt");
}
my $first=(split("e-",$expect))[0];
my $second=(split("e-",$expect))[1];
print $tfh join("\t",
$hsp->feature1->seq_id,
$hsp->feature2->seq_id,
int($first),
int($second) ), "\n";
$count++;
}
}
}
return $count;
}
=head2 _parse_blastfile
Title : _parse_blastfile
Usage : $self->_parse_blastfile()
Function: internal function for quickly parsing blast evalue
scores from raw blast output file
Returns : array ref to ids and score [protein1 protein2 magnitude factor]
Args : file path
=cut
sub _parse_blastfile {
my ($self, $file,$tfh) = @_;
open(FILE,$file) || $self->throw("Cannot open Blast Output File");
my ($query,$reference,$first,$second);
my @array;
my $count;
my $weight = $self->weight;
while(<FILE>){
if(/Query=\s+(\S+)/){
$query = $1;
}
if(/^>(\S+)/){
$reference = $1;
}
if (/Expect = (\S+)/){
my $raw=$1;
$raw=~s/^e-/1e-/g;
my $expect=sprintf("%e",$raw);
if ($expect==0){
$expect=sprintf("%e","1e-$weight");
}
$first=(split("e-",$expect))[0];
$second=(split("e-",$expect))[1];
print $tfh join("\t", $query,
$reference,
int($first),
int($second)), "\n";
$count++;
}
}
return $count;
}
=head2 _parse_mcl
Title : _parse_mcl
Usage : $self->_parse_mcl()
Function: internal function for quickly parsing mcl output and
generating the array of clusters
Returns : Array Ref of clustered Ids
Args : index file path, mcl output file path
=cut
sub _parse_mcl {
my ($self,$ind,$mcl) = @_;
open (MCL,$mcl) || $self->throw("Error, cannot open $mcl for parsing");
my $i =-1;
my $start;
my (@cluster,@out);
while(<MCL>) {
if ($start) {
chomp($_);
$cluster[$i] = join(" ",$cluster[$i],"$_");
}
if(/^\d+/){
$start = 1;
$i++;
$cluster[$i] = join(" ",$cluster[$i] || '',"$_");
}
if (/\$$/){
$start = 0;
}
last if /^\(mclruninfo/;
}
open (IND,$ind) || $self->throw("Cannot open $ind for parsing");
my %hash;
while(<IND>){
/^(\S+)\s+(\S+)/;
$hash{$1}=$2;
}
for (my $j=0;$j<$i+1;$j++) {
my @array=split(" ",$cluster[$j]);
for (my $p=1;$p<$#array;$p++){
push @{$out[$array[0]]}, $hash{$array[$p]};
}
}
return \@out;
}
1;